Ill make it clear i will hate the levelling system in any implementation, and it should be replaced with an improved perk system similar to what we already have, but regardless, perks need an overall as being forced to use specific perks sucks, especially for ones like magnetism. Here is my proposed rework:
Perks are now split into Dominant Perks, and Recessive perks (based on genetic inheritence) and are now manually equiped to plants once unlocked:
Dominant perks are specific to a plant, and are unlocked through levelling like normal (if levelling gets replaced, this replaces the stat increases completly). They can only be equipped to a teir 1 plant. However, their fusions will inheret them. The way the inheritence works is that if two plants have two different dominant perks, the fusion will have both of them, but if they both have the same perk, it instead gets upgraded. This would add much more strategy, and make levelling less artificial. Upgrading teir 2 and 3 plants will grant even more dominant perks more suited towards them, that can be equipped to any of the teir 1 plants used to make it. Current examples are critical hits and bouncy cabbage.
Recessive perks are less impactful, but one can be equipped to any plant without restriction (with exceptions for some). These are not passed on, and are instead equipped to each fusion and plant individually. An example is the ghost pepper perk which could be equipped to any plant. These can be obtained from the shop, plant pass, level progression, or any other means. As for the exceptions, teir 2 and 3 plants could award a special recessive perks exclusive to their teir 2 and 3 fusions for upgrading them (e.g peanut and three peanut). This would add more value to upgrading them.
Overall, i wish for this to be added. If it replaces levelling, it would be fanastic as unlocking perks is significantly more interesting than stat increases, and also advances your strategy, as you are locked to 1 dominant perk for teir 1s, and 1 recessive perk for any plant. This adds more value to fusion, as the higher the teir the fusion, the more it will benifit from dominant perks due to the inheritence system, which could be an alternative to boosting their stats drastically. Even if this doesnt replace levelling, a perk rework like this is needed.
Edit: As for zombies, they could have perks too as a replacement for levelling. E.g bring back the occasional 20% more damage and movement speed, and add more interesting ones like "All zombies spawn a water tile on death", "Screendoors leave tombstones in their path" or something. But not every level should have perks. These would help with the repetitive nature of the game and add unique challenges.